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Receptor Information

>6upy Chain B (length=1109) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
ILYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKR
TKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVL
IAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGRE
GSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLE
MLKPCVEDGFVIQDRETALDFIGKEKRIQYAKDILQKEFLPHITQLEGFE
SRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLF
KKLTKDIFRYMQRTVEELAINAKTITSGLKYALATGNWGEQKKAMSSRAG
VSQVLNRYTYSSTLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQACG
LVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNG
VWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVY
RPLFIVEDDGHKELKVRKGHIAKLMATEYQDVEEYTWSSLLNEGLVEYID
AEEEESILIAMQPEDLEPLDVDPAKRIRVSHHATTFTHCEIHPSMILGVA
ASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKP
LGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFR
SLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPG
VRVSGEDVIIGKTTPISAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLK
FVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLII
NPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREH
GYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQ
VLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHI
CGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNI
TPRLYTDRS

Ligand ID

APC

InChI

InChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-29(19,20)4-30(21,22)28-31(23,24)25/h2-3,5,7-8,11,17-18H,1,4H2,(H,19,20)(H,21,22)(H2,12,13,14)(H2,23,24,25)/t5-,7-,8-,11-/m1/s1

InChIKey

CAWZRIXWFRFUQB-IOSLPCCCSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OP(=O)(O)O)O)O)O)N
CACTVS 3.341	Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N
ACDLabs 10.04	O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341	Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O

Formula

C11 H18 N5 O12 P3

Name

DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER;
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE

PDB chain

6upy Chain B Residue 1301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	6upy RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions.
Resolution	3.4 Å
Binding residue (original residue number in PDB)	S1019 R1020
Binding residue (residue number reindexed from 1)	S907 R908
Annotation score	1

Enzyme Commision number

2.7.7.6: DNA-directed RNA polymerase.

	Molecular Function
GO:0001055	RNA polymerase II activity
GO:0003677	DNA binding
GO:0003729	mRNA binding
GO:0003899	DNA-directed 5'-3' RNA polymerase activity
GO:0003968	RNA-dependent RNA polymerase activity
GO:0005515	protein binding
GO:0008270	zinc ion binding
GO:0016779	nucleotidyltransferase activity
GO:0032549	ribonucleoside binding
GO:0034062	5'-3' RNA polymerase activity
GO:0046872	metal ion binding

	Biological Process
GO:0001172	RNA-templated transcription
GO:0006351	DNA-templated transcription
GO:0006366	transcription by RNA polymerase II
GO:0006367	transcription initiation at RNA polymerase II promoter
GO:0006368	transcription elongation by RNA polymerase II

	Cellular Component
GO:0000428	DNA-directed RNA polymerase complex
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005665	RNA polymerase II, core complex
GO:0005739	mitochondrion
GO:0010494	cytoplasmic stress granule

PDB	RCSB:6upy, PDBe:6upy, PDBj:6upy
PDBsum	6upy
PubMed	32284409
UniProt	P08518\|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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Structure of PDB 6upy Chain B Binding Site BS03